Molecular dynamics simulations of biomolecules

By B. Geisbrecht, S. Gould, J. Berg. 2002

3,253 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

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Citations in the corpus

Evolutionary context-integrated deep sequence modeling for protein engineering (2020, background): “Rational design is oftentimes assisted by quantitative approaches to evaluate sequences that fold into a specific structure, including biophysical modeling [3,4] , force field approximations [5–7] , structure prediction [8–10] , and molecular dynamics simulations [11] .”
The role of dynamics in allosteric regulation. (2003, background): “putational approaches for the study of protein dynamics push simulations into time regimes that have previously not been accessible [23].”
Enhancing structure prediction and design of soluble and membrane proteins with explicit solvent-protein interactions (2017, background): “Modeling protein structure and solvent environment at atomic resolution represents one key application of molecular dynamic simulations techniques (Karplus and McCammon, 2002).”
Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS (2004, background): “MD simulations are increasingly proving their worth for the fuller understanding of biomolecular structure and dynamics (Karplus & McCammon 2002).”
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures (2012, background): “their characteristics may change significantly over time [14,17,31,32].”
Molecular and Cellular Biophysics: Index (2006, methodology): “These kinds of computer simulations have been widely used to study rapid processes occurring on timescales of up to nanoseconds (Karplus, 2002).”
Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection (2017, methodology): “To study the physical basis of function and structure of biological macromolecules molecular dynamics (MD) simulation was used 53–59 .”